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Change Fortran wrapper building script (wrappers/FortranWrapper_Header.xslt) to add line breaks between function and subroutine arguments.  This was needed to keep lines under 132 characters in length

Changed std::fabs to std::abs in AssertionUtilities.h to avoid compile ambiguity error on Windows with TestReferenceCustomHbondForce

Downgraded recent cmake changes to ghastly compliance with cmake 2.4, for the benefit of the simtk dart server.

Modified Cuda FreeEnergy plugin to use a different windows export macro than main openmm library and cuda library.
Modified CUDA_NVCC_FLAGS to be consistent with Peter's latest version in all three locations they are defined.
Added "-Xcompiler '/MD'" to CUDA_NVCC_FLAGS on Windows to avoid link error in Cuda FreeEnergy plugin.

Export CudaFreeEnergyKernelFactory symbols to avoid link error in test program.

So far tested only on GPU-having windows machine.